Starting phenix.real_space_refine on Wed Sep 25 18:54:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/09_2024/6k7i_9934.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/09_2024/6k7i_9934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/09_2024/6k7i_9934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/09_2024/6k7i_9934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/09_2024/6k7i_9934.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7i_9934/09_2024/6k7i_9934.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 56 5.16 5 C 6857 2.51 5 N 1753 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7853 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 30, 'TRANS': 955} Chain breaks: 3 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.40, per 1000 atoms: 0.60 Number of scatterers: 10590 At special positions: 0 Unit cell: (72.21, 112.88, 168.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 3 15.00 O 1921 8.00 N 1753 7.00 C 6857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 47.8% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.628A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.525A pdb=" N ALA A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.213A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.361A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.850A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 600 through 617 removed outlier: 4.617A pdb=" N SER A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.575A pdb=" N LEU A 622 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 681 removed outlier: 4.490A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.585A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 833 removed outlier: 4.349A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 856 removed outlier: 4.092A pdb=" N ASN A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.699A pdb=" N TRP A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.185A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.650A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.419A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 4.066A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.942A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix removed outlier: 3.520A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.002A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.639A pdb=" N GLU A 144 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN A 136 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 169 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.554A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 780 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 425 removed outlier: 6.101A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 647 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU A 638 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 596 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 640 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 544 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN A 530 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.621A pdb=" N PHE A 507 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 517 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 509 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.715A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.473A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.503A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1784 1.32 - 1.44: 2914 1.44 - 1.57: 6050 1.57 - 1.69: 6 1.69 - 1.82: 87 Bond restraints: 10841 Sorted by residual: bond pdb=" O2B ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.507 1.614 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O3A ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.698 1.603 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 ACP A1201 " pdb=" C5 ACP A1201 " ideal model delta sigma weight residual 1.386 1.469 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3G ACP A1201 " pdb=" PG ACP A1201 " ideal model delta sigma weight residual 1.532 1.607 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 ACP A1201 " pdb=" C6 ACP A1201 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 10836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 14080 2.90 - 5.81: 552 5.81 - 8.71: 69 8.71 - 11.61: 17 11.61 - 14.52: 4 Bond angle restraints: 14722 Sorted by residual: angle pdb=" C LEU A 687 " pdb=" N LYS A 688 " pdb=" CA LYS A 688 " ideal model delta sigma weight residual 121.54 134.13 -12.59 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C SER A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 120.97 135.49 -14.52 2.84e+00 1.24e-01 2.61e+01 angle pdb=" C PRO A 384 " pdb=" N THR A 385 " pdb=" CA THR A 385 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LYS A 688 " pdb=" N LYS A 689 " pdb=" CA LYS A 689 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ALA A 57 " pdb=" N LYS A 58 " pdb=" CA LYS A 58 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 ... (remaining 14717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 6025 22.47 - 44.94: 486 44.94 - 67.40: 49 67.40 - 89.87: 15 89.87 - 112.34: 3 Dihedral angle restraints: 6578 sinusoidal: 2755 harmonic: 3823 Sorted by residual: dihedral pdb=" CA ARG A 510 " pdb=" C ARG A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 144.75 35.25 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N SER A 683 " pdb=" CA SER A 683 " ideal model delta harmonic sigma weight residual 180.00 147.44 32.56 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA PHE A 534 " pdb=" C PHE A 534 " pdb=" N THR A 535 " pdb=" CA THR A 535 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 6575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1415 0.100 - 0.199: 244 0.199 - 0.298: 19 0.298 - 0.398: 3 0.398 - 0.497: 2 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CB THR A 511 " pdb=" CA THR A 511 " pdb=" OG1 THR A 511 " pdb=" CG2 THR A 511 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1680 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.356 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.254 2.00e-02 2.50e+03 2.11e-01 5.58e+02 pdb=" C7 NAG C 402 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.351 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.167 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" C7 NAG C 401 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.225 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.019 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2461 2.78 - 3.31: 9477 3.31 - 3.84: 17662 3.84 - 4.37: 21051 4.37 - 4.90: 36325 Nonbonded interactions: 86976 Sorted by model distance: nonbonded pdb=" O ASP A 409 " pdb=" OG1 THR A 413 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 670 " pdb=" N GLY A 671 " model vdw 2.309 3.120 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.310 3.040 nonbonded pdb=" O TYR A 573 " pdb=" OG1 THR A 577 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 394 " pdb=" ND2 ASN A 397 " model vdw 2.316 3.120 ... (remaining 86971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.128 10841 Z= 0.955 Angle : 1.315 14.519 14722 Z= 0.692 Chirality : 0.076 0.497 1683 Planarity : 0.013 0.306 1832 Dihedral : 15.636 112.339 4103 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.92 % Favored : 90.69 % Rotamer: Outliers : 0.78 % Allowed : 8.43 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.18), residues: 1300 helix: -2.90 (0.15), residues: 587 sheet: -1.92 (0.38), residues: 149 loop : -3.13 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 860 HIS 0.009 0.002 HIS A 124 PHE 0.039 0.004 PHE C 304 TYR 0.035 0.004 TYR A 59 ARG 0.016 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6687 (mmtt) cc_final: 0.4681 (mttm) REVERT: A 392 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7326 (mtt-85) REVERT: A 663 ASP cc_start: 0.7688 (t70) cc_final: 0.7299 (t0) REVERT: A 693 MET cc_start: 0.1202 (mmt) cc_final: -0.0638 (tpp) REVERT: A 727 LEU cc_start: 0.6848 (mp) cc_final: 0.6625 (mt) REVERT: A 732 LYS cc_start: 0.7982 (mttm) cc_final: 0.7328 (tptp) REVERT: A 1013 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8018 (pp) REVERT: C 151 LEU cc_start: 0.8640 (mt) cc_final: 0.8423 (mt) REVERT: C 184 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8052 (mt-10) REVERT: C 337 PHE cc_start: 0.8131 (t80) cc_final: 0.7924 (t80) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.2573 time to fit residues: 49.9999 Evaluate side-chains 114 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 124 HIS A 134 GLN A 279 ASN A 320 ASN A 381 HIS A 434 ASN A 679 ASN A 813 ASN C 36 GLN C 131 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10841 Z= 0.202 Angle : 0.707 9.586 14722 Z= 0.362 Chirality : 0.048 0.463 1683 Planarity : 0.005 0.049 1832 Dihedral : 10.862 107.617 1632 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 2.26 % Allowed : 10.96 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.20), residues: 1300 helix: -1.28 (0.19), residues: 572 sheet: -1.42 (0.40), residues: 144 loop : -2.73 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 682 PHE 0.023 0.001 PHE A 368 TYR 0.014 0.001 TYR A 59 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6433 (mmtt) cc_final: 0.4539 (mttt) REVERT: A 390 MET cc_start: 0.7013 (ttt) cc_final: 0.6596 (ttm) REVERT: A 663 ASP cc_start: 0.7796 (t0) cc_final: 0.7359 (t0) REVERT: A 693 MET cc_start: 0.1350 (mmt) cc_final: -0.0476 (tpp) REVERT: A 732 LYS cc_start: 0.7918 (mttm) cc_final: 0.7359 (tptp) REVERT: A 747 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.6054 (mm) REVERT: A 831 ILE cc_start: 0.8374 (pt) cc_final: 0.7976 (mt) REVERT: A 874 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: A 1013 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7452 (pp) REVERT: C 102 CYS cc_start: 0.6526 (p) cc_final: 0.6225 (p) REVERT: C 184 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 337 PHE cc_start: 0.7950 (t80) cc_final: 0.7748 (t80) outliers start: 26 outliers final: 6 residues processed: 144 average time/residue: 0.2583 time to fit residues: 51.4414 Evaluate side-chains 117 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 813 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10841 Z= 0.216 Angle : 0.671 9.153 14722 Z= 0.341 Chirality : 0.047 0.376 1683 Planarity : 0.004 0.056 1832 Dihedral : 10.307 97.900 1626 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.17 % Allowed : 13.22 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.22), residues: 1300 helix: -0.57 (0.20), residues: 569 sheet: -1.26 (0.40), residues: 147 loop : -2.51 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 682 PHE 0.019 0.001 PHE A 368 TYR 0.013 0.001 TYR C 297 ARG 0.004 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6379 (mmtt) cc_final: 0.4522 (mttt) REVERT: A 260 THR cc_start: 0.3255 (OUTLIER) cc_final: 0.2829 (p) REVERT: A 263 VAL cc_start: 0.6262 (OUTLIER) cc_final: 0.5917 (m) REVERT: A 392 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7648 (mtt90) REVERT: A 663 ASP cc_start: 0.7853 (t0) cc_final: 0.7426 (t0) REVERT: A 693 MET cc_start: 0.1000 (mmt) cc_final: -0.0771 (tpp) REVERT: A 732 LYS cc_start: 0.7899 (mttm) cc_final: 0.7374 (tptp) REVERT: A 747 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6155 (mm) REVERT: A 826 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8017 (ttmm) REVERT: A 831 ILE cc_start: 0.8371 (pt) cc_final: 0.8020 (mt) REVERT: A 874 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: A 1013 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7499 (pp) REVERT: C 102 CYS cc_start: 0.6528 (p) cc_final: 0.6261 (p) REVERT: C 184 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 337 PHE cc_start: 0.7962 (t80) cc_final: 0.7722 (t80) outliers start: 25 outliers final: 8 residues processed: 133 average time/residue: 0.2520 time to fit residues: 46.8271 Evaluate side-chains 114 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10841 Z= 0.309 Angle : 0.692 9.454 14722 Z= 0.352 Chirality : 0.049 0.373 1683 Planarity : 0.004 0.047 1832 Dihedral : 10.003 95.126 1625 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.35 % Allowed : 15.48 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.22), residues: 1300 helix: -0.45 (0.20), residues: 585 sheet: -1.28 (0.40), residues: 152 loop : -2.35 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 927 HIS 0.005 0.001 HIS A 682 PHE 0.019 0.002 PHE A 368 TYR 0.016 0.002 TYR C 297 ARG 0.004 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6325 (mmtt) cc_final: 0.4423 (mttt) REVERT: A 260 THR cc_start: 0.3255 (OUTLIER) cc_final: 0.2887 (p) REVERT: A 263 VAL cc_start: 0.6255 (OUTLIER) cc_final: 0.5921 (m) REVERT: A 644 ILE cc_start: 0.2336 (OUTLIER) cc_final: 0.2057 (pt) REVERT: A 663 ASP cc_start: 0.7922 (t0) cc_final: 0.7534 (t0) REVERT: A 693 MET cc_start: 0.0829 (mmt) cc_final: -0.0898 (tpp) REVERT: A 732 LYS cc_start: 0.7930 (mttm) cc_final: 0.7363 (tptp) REVERT: A 747 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6106 (mm) REVERT: A 874 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: A 1013 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7540 (pp) REVERT: C 102 CYS cc_start: 0.6517 (p) cc_final: 0.6268 (p) REVERT: C 184 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7832 (mt-10) REVERT: C 337 PHE cc_start: 0.8011 (t80) cc_final: 0.7741 (t80) outliers start: 27 outliers final: 12 residues processed: 128 average time/residue: 0.2317 time to fit residues: 42.2131 Evaluate side-chains 115 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0470 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 0.0010 overall best weight: 0.4286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 323 HIS C 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10841 Z= 0.148 Angle : 0.608 11.196 14722 Z= 0.306 Chirality : 0.044 0.265 1683 Planarity : 0.004 0.044 1832 Dihedral : 9.017 92.531 1625 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.17 % Allowed : 17.39 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1300 helix: 0.15 (0.21), residues: 575 sheet: -1.01 (0.40), residues: 157 loop : -2.14 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 832 PHE 0.015 0.001 PHE A 368 TYR 0.010 0.001 TYR C 121 ARG 0.004 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.182 Fit side-chains REVERT: A 60 ASN cc_start: 0.7068 (t0) cc_final: 0.6774 (t0) REVERT: A 207 LYS cc_start: 0.6192 (mmtt) cc_final: 0.4331 (mttt) REVERT: A 275 LYS cc_start: 0.6391 (mmtm) cc_final: 0.6121 (mmtm) REVERT: A 493 GLU cc_start: 0.6933 (tp30) cc_final: 0.6625 (tt0) REVERT: A 644 ILE cc_start: 0.2243 (OUTLIER) cc_final: 0.1975 (pt) REVERT: A 663 ASP cc_start: 0.7808 (t0) cc_final: 0.7440 (t0) REVERT: A 693 MET cc_start: 0.0858 (mmt) cc_final: -0.0870 (tpp) REVERT: A 732 LYS cc_start: 0.7729 (mttm) cc_final: 0.7244 (tptp) REVERT: A 747 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6100 (mm) REVERT: A 874 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: A 900 CYS cc_start: 0.6950 (m) cc_final: 0.6742 (t) REVERT: A 1013 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7431 (pp) REVERT: C 92 ASN cc_start: 0.8937 (t0) cc_final: 0.8734 (t0) REVERT: C 102 CYS cc_start: 0.6597 (p) cc_final: 0.6329 (p) REVERT: C 152 ASN cc_start: 0.7790 (t0) cc_final: 0.7450 (t0) REVERT: C 184 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 337 PHE cc_start: 0.7984 (t80) cc_final: 0.7735 (t80) outliers start: 25 outliers final: 8 residues processed: 131 average time/residue: 0.2504 time to fit residues: 46.1126 Evaluate side-chains 113 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 40.0000 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.0470 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10841 Z= 0.198 Angle : 0.618 9.372 14722 Z= 0.312 Chirality : 0.045 0.304 1683 Planarity : 0.004 0.045 1832 Dihedral : 8.595 88.884 1625 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.09 % Allowed : 17.65 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1300 helix: 0.27 (0.21), residues: 576 sheet: -0.86 (0.42), residues: 150 loop : -2.05 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.011 0.001 TYR C 297 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6208 (mmtt) cc_final: 0.4342 (mttt) REVERT: A 275 LYS cc_start: 0.6343 (mmtm) cc_final: 0.5911 (mmtm) REVERT: A 493 GLU cc_start: 0.6976 (tp30) cc_final: 0.6653 (tt0) REVERT: A 644 ILE cc_start: 0.2218 (OUTLIER) cc_final: 0.1956 (pt) REVERT: A 663 ASP cc_start: 0.7845 (t0) cc_final: 0.7441 (t0) REVERT: A 693 MET cc_start: 0.0780 (mmt) cc_final: -0.0886 (tpp) REVERT: A 732 LYS cc_start: 0.7607 (mttm) cc_final: 0.7148 (tptp) REVERT: A 747 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6074 (mm) REVERT: A 874 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: A 1013 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7481 (pp) REVERT: C 102 CYS cc_start: 0.6635 (p) cc_final: 0.6370 (p) REVERT: C 152 ASN cc_start: 0.7795 (t0) cc_final: 0.7460 (t0) REVERT: C 184 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 337 PHE cc_start: 0.8006 (t80) cc_final: 0.7699 (t80) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 0.2321 time to fit residues: 40.3358 Evaluate side-chains 114 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10841 Z= 0.170 Angle : 0.612 9.103 14722 Z= 0.306 Chirality : 0.045 0.296 1683 Planarity : 0.004 0.046 1832 Dihedral : 8.376 86.637 1625 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.48 % Allowed : 18.26 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1300 helix: 0.40 (0.22), residues: 577 sheet: -0.90 (0.41), residues: 153 loop : -1.98 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.013 0.001 PHE A 368 TYR 0.011 0.001 TYR A 59 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6209 (mmtt) cc_final: 0.4325 (mttt) REVERT: A 644 ILE cc_start: 0.2292 (OUTLIER) cc_final: 0.2053 (pt) REVERT: A 663 ASP cc_start: 0.7740 (t0) cc_final: 0.7375 (t0) REVERT: A 693 MET cc_start: 0.0956 (mmt) cc_final: -0.0801 (tpp) REVERT: A 732 LYS cc_start: 0.7588 (mttm) cc_final: 0.7146 (tptp) REVERT: A 747 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6065 (mm) REVERT: A 874 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: A 1013 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7457 (pp) REVERT: C 102 CYS cc_start: 0.6636 (p) cc_final: 0.6370 (p) REVERT: C 152 ASN cc_start: 0.7769 (t0) cc_final: 0.7439 (t0) REVERT: C 184 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 337 PHE cc_start: 0.7995 (t80) cc_final: 0.7699 (t80) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 0.2565 time to fit residues: 39.1280 Evaluate side-chains 110 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 277 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 810 GLN C 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10841 Z= 0.214 Angle : 0.625 9.204 14722 Z= 0.313 Chirality : 0.045 0.294 1683 Planarity : 0.004 0.047 1832 Dihedral : 8.229 81.726 1625 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.83 % Allowed : 18.78 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.23), residues: 1300 helix: 0.39 (0.22), residues: 575 sheet: -0.81 (0.42), residues: 150 loop : -1.94 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.012 0.001 TYR C 297 ARG 0.005 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6226 (mmtt) cc_final: 0.4341 (mttt) REVERT: A 644 ILE cc_start: 0.2283 (OUTLIER) cc_final: 0.2061 (pt) REVERT: A 663 ASP cc_start: 0.7755 (t0) cc_final: 0.7343 (t0) REVERT: A 693 MET cc_start: 0.0887 (mmt) cc_final: -0.0836 (tpp) REVERT: A 732 LYS cc_start: 0.7536 (mttm) cc_final: 0.7109 (tptp) REVERT: A 747 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.6034 (mm) REVERT: A 874 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: A 1013 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7440 (pp) REVERT: C 102 CYS cc_start: 0.6696 (p) cc_final: 0.6430 (p) REVERT: C 184 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7879 (mt-10) REVERT: C 337 PHE cc_start: 0.8026 (t80) cc_final: 0.7725 (t80) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.2404 time to fit residues: 38.1370 Evaluate side-chains 112 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10841 Z= 0.235 Angle : 0.632 9.342 14722 Z= 0.317 Chirality : 0.046 0.294 1683 Planarity : 0.004 0.046 1832 Dihedral : 8.119 77.433 1625 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.91 % Allowed : 18.61 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1300 helix: 0.31 (0.21), residues: 582 sheet: -0.91 (0.40), residues: 161 loop : -1.98 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.015 0.001 PHE A 368 TYR 0.013 0.001 TYR A 59 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6185 (mmtt) cc_final: 0.4278 (mttt) REVERT: A 541 MET cc_start: 0.4449 (ptt) cc_final: 0.4232 (ptt) REVERT: A 644 ILE cc_start: 0.2322 (OUTLIER) cc_final: 0.2110 (pt) REVERT: A 663 ASP cc_start: 0.7747 (t0) cc_final: 0.7314 (t0) REVERT: A 693 MET cc_start: 0.0923 (mmt) cc_final: -0.0791 (tpp) REVERT: A 732 LYS cc_start: 0.7540 (mttm) cc_final: 0.7103 (tptp) REVERT: A 747 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5993 (mm) REVERT: A 874 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: A 1013 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7509 (pp) REVERT: C 102 CYS cc_start: 0.6678 (p) cc_final: 0.6410 (p) REVERT: C 184 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7880 (mt-10) REVERT: C 337 PHE cc_start: 0.8034 (t80) cc_final: 0.7729 (t80) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.2348 time to fit residues: 38.5230 Evaluate side-chains 116 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10841 Z= 0.152 Angle : 0.596 9.171 14722 Z= 0.298 Chirality : 0.044 0.294 1683 Planarity : 0.004 0.046 1832 Dihedral : 7.738 68.878 1625 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.83 % Allowed : 18.78 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1300 helix: 0.62 (0.22), residues: 576 sheet: -0.78 (0.40), residues: 162 loop : -1.93 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.002 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.010 0.001 TYR C 121 ARG 0.003 0.000 ARG C 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.6161 (mmtt) cc_final: 0.4262 (mttt) REVERT: A 541 MET cc_start: 0.4541 (ptt) cc_final: 0.4338 (ptt) REVERT: A 644 ILE cc_start: 0.2283 (OUTLIER) cc_final: 0.2071 (pt) REVERT: A 663 ASP cc_start: 0.7728 (t0) cc_final: 0.7482 (t0) REVERT: A 693 MET cc_start: 0.0860 (mmt) cc_final: -0.0809 (tpp) REVERT: A 732 LYS cc_start: 0.7457 (mttm) cc_final: 0.7053 (tptp) REVERT: A 747 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5991 (mm) REVERT: A 874 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: A 1013 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7459 (pp) REVERT: C 102 CYS cc_start: 0.6730 (p) cc_final: 0.6445 (p) REVERT: C 152 ASN cc_start: 0.7797 (t0) cc_final: 0.7474 (t0) REVERT: C 184 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7874 (mt-10) REVERT: C 337 PHE cc_start: 0.7995 (t80) cc_final: 0.7676 (t80) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.2428 time to fit residues: 38.4108 Evaluate side-chains 112 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.216011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.186717 restraints weight = 10421.092| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.34 r_work: 0.3801 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10841 Z= 0.164 Angle : 0.595 9.070 14722 Z= 0.297 Chirality : 0.044 0.314 1683 Planarity : 0.004 0.046 1832 Dihedral : 7.390 66.514 1625 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.65 % Allowed : 19.04 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1300 helix: 0.62 (0.22), residues: 579 sheet: -0.70 (0.40), residues: 162 loop : -1.91 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.012 0.001 PHE A 368 TYR 0.011 0.001 TYR A 59 ARG 0.003 0.000 ARG C 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.11 seconds wall clock time: 39 minutes 55.20 seconds (2395.20 seconds total)